Hi Rosalia,

What version of perl are you using? Based on this thread from last year - https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-May/045407.html - it seems like this is a known issue with new versions of perl and freesurfer v5.3. Unfortunately, your only two options are to install an older version of perl (5.10 should be old enough): https://stackoverflow.com/questions/16147120/how-can-i-install-another-versi...

or install freesurfer v6.0: https://surfer.nmr.mgh.harvard.edu/fswiki/Download

best, Andrew

On Nov 13, 2017, at 11:13 AM, Douglas N Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:

Is this happening on all subjects or just this one? If just this one, have you looked at the images to make sure that there is nothing really wrong?

On 11/12/2017 12:56 PM, Rosalia Dacosta Aguayo wrote: My apologizes,

I missed forgot to include the following information:

1. FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 2. Platform: CentOS release 6.7 3. uname -a: Linux rosalia-PORTEGE-Z930 4.4.0-98-generic #121-Ubuntu SMP Tue Oct 10 14:24:03 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux 4. Recon-all.log: see attached

2017-11-12 18:50 GMT+01:00 Rosalia Dacosta Aguayo <rdacostaa@gmail.commailto:rdacostaa@gmail.com mailto:rdacostaa@gmail.com>:

​Hello FreeSurfer Developers,

I am attempting ​to compute autorecon1 in a subject to see how it works recon-all in a stepwise as described in the tutorial. Sorry if this is a very naive question but it is the first time I am trying to run an analysis with FreeSurfer.

After running: /*r*/*/econ-all -subjid 001 -autorecon1 -i S_001.nii.gz/ *

I have found that it crashes with the following warning: *recon-all -s 001 exited with ERRORS at dom * I have seen that the problem comes from orig_nu.log

Does anyone have any thoughts on how to trouble-shoot this problem? I have attached the recon-all.log and the orig_nu.log in case it is of any use.

Kind regards, Rosalia

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